#ifndef READ_SIMULATOR_H_
#define READ_SIMULATOR_H_

#include <string>
#include <vector>
#include <iostream>
#include <fstream>
#include "RefDB.h"
#include <math.h>
#include <map>
#include <sstream>
#include <algorithm>
#include <cstring>
#include <cstdlib>
#include <time.h>
using namespace std;

class readSimulator{
public:
	readSimulator();
	~readSimulator();


	void genReads(string refFileName, unsigned int NumOfReads, unsigned int LengthOfReads, unsigned int Errors, unsigned int NumOfChromosomes, string OutputFile, string configFile);
	string replaceBaseUniformly(string realSeq);
	char findReplacement(char base);
	bool checkIfCorrectSeq(string seq);

	//data
	vector<int> intervals;
private:

	//pointer for writing
	ofstream writeFile;
	ifstream readConfigFile;

};
#endif
